Merge pull request #2658 from nipy/rel/1.1.1

REL: 1.1.1

Author: effigies

.zenodo.json

@@ -30,16 +30,16 @@
       "name": "Notter, Michael Philipp",
       "orcid": "0000-0002-5866-047X"
     },
-    {
-      "affiliation": "MIT",
-      "name": "Jarecka, Dorota",
-      "orcid": "0000-0003-1857-8129"
-    },
     {
       "affiliation": "University of Iowa",
       "name": "Johnson, Hans",
       "orcid": "0000-0001-9513-2660"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Jarecka, Dorota",
+      "orcid": "0000-0003-1857-8129"
+    },
     {
       "name": "Burns, Christopher"
     },
@@ -60,16 +60,16 @@
       "name": "Salo, Taylor",
       "orcid": "0000-0001-9813-3167"
     },
-    {
-      "affiliation": "University of California, San Francisco",
-      "name": "Jordan, Kesshi",
-      "orcid": "0000-0001-6313-0580"
-    },
     {
       "affiliation": "MIT",
       "name": "Goncalves, Mathias",
       "orcid": "0000-0002-7252-7771"
     },
+    {
+      "affiliation": "University of California, San Francisco",
+      "name": "Jordan, Kesshi",
+      "orcid": "0000-0001-6313-0580"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Waskom, Michael"
@@ -151,6 +151,11 @@
       "name": "Cipollini, Ben",
       "orcid": "0000-0002-7782-0790"
     },
+    {
+      "affiliation": "Dartmouth College: Hanover, NH, United States",
+      "name": "Halchenko, Yaroslav O.",
+      "orcid": "0000-0003-3456-2493"
+    },
     {
       "affiliation": "Montreal Neurological Institute and Hospital",
       "name": "Markello, Ross",
@@ -164,11 +169,6 @@
     {
       "name": "Moloney, Brendan"
     },
-    {
-      "affiliation": "Dartmouth College: Hanover, NH, United States",
-      "name": "Halchenko, Yaroslav O.",
-      "orcid": "0000-0003-3456-2493"
-    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann , Demian",
@@ -325,9 +325,6 @@
     {
       "name": "Millman, Jarrod"
     },
-    {
-      "name": "Haehn, Daniel"
-    },
     {
       "name": "Lai, Jeff"
     },
@@ -449,6 +446,9 @@
     {
       "name": "Mertz, Fred"
     },
+    {
+      "name": "Haehn, Daniel"
+    },
     {
       "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
       "name": "Geisler, Daniel",

doc/changelog/1.X.X-changelog

@@ -1,3 +1,25 @@
+1.1.1 (July 30, 2018)
+=====================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/22?closed=1)
+
+  * FIX: Un-set incorrect default options in TOPUP (https://github.com/nipy/nipype/pull/2637)
+  * FIX: Copy FSCommand.version to ReconAll.version (https://github.com/nipy/nipype/pull/2656)
+  * FIX: Various BIDSDataGrabber fixes (https://github.com/nipy/nipype/pull/2651)
+  * FIX: changing Node._output_dir to realpath (https://github.com/nipy/nipype/pull/2639)
+  * FIX: Typo in DWIExtract of Mrtrix3interface (https://github.com/nipy/nipype/pull/2634)
+  * FIX: Typo in FSLXCommandInputSpec (https://github.com/nipy/nipype/pull/2628)
+  * ENH: Allow transform to be saved from AFNI 3dWarp (https://github.com/nipy/nipype/pull/2642)
+  * ENH: Allow BIDS-style slice timings to be passed directly to TShift  (https://github.com/nipy/nipype/pull/2608)
+  * ENH: S3 access using instance role (https://github.com/nipy/nipype/pull/2621)
+  * ENH Minor improvements to PR template (https://github.com/nipy/nipype/pull/2636)
+  * TEST: make specs (https://github.com/nipy/nipype/pull/2653)
+  * DOC: update neurodocker tutorial for neurodocker version 0.4.0 (https://github.com/nipy/nipype/pull/2647)
+  * MAINT: Remove vestiges of nose testing library (https://github.com/nipy/nipype/pull/2662)
+  * MAINT: Make pytest-xdist a dependency (https://github.com/nipy/nipype/pull/2649)
+  * CI: Install pytest>=3.4 in Travis (https://github.com/nipy/nipype/pull/2659)
+
+
 1.1.0 (July 04, 2018)
 =====================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.1.0"
+release = "1.1.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.0.3 <http://nipype.readthedocs.io/en/1.0.3/>`_ `1.0.2 <http://nipype.readthedocs.io/en/1.0.2/>`_
+Previous versions: `1.1.0 <http://nipype.readthedocs.io/en/1.1.0/>`_ `1.0.4 <http://nipype.readthedocs.io/en/1.0.4/>`_
 
 
 .. container:: doc2

nipype/info.py

@@ -11,7 +11,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '1.1.1-dev'
+__version__ = '1.1.1'
 
 
 def get_nipype_gitversion():

nipype/interfaces/ants/registration.py

@@ -125,7 +125,7 @@ class ANTSOutputSpec(TraitedSpec):
 
 
 class ANTS(ANTSCommand):
-    """ANTS wrapper for registration of images 
+    """ANTS wrapper for registration of images
     (old, use Registration instead)
 
     Examples

nipype/interfaces/io.py

@@ -124,7 +124,7 @@ def add_traits(base, names, trait_type=None):
 
 
 def _get_head_bucket(s3_resource, bucket_name):
-    """ Try to get the header info of a bucket, in order to 
+    """ Try to get the header info of a bucket, in order to
     check if it exists and its permissions
     """
 

nipype/utils/filemanip.py

@@ -662,7 +662,7 @@ def loadpkl(infile, versioning=False):
 
         return unpkl
 
-    # Unpickling problems    
+    # Unpickling problems
     except Exception as e:
         if not versioning:
             raise e

nipype/utils/tests/test_filemanip.py

@@ -547,7 +547,7 @@ class PickledBreaker:
     def __setstate__(self, d):
         raise Exception()
 
-        
+
 def test_versioned_pklization(tmpdir):
     tmpdir.chdir()
 
@@ -560,7 +560,7 @@ def test_versioned_pklization(tmpdir):
 
             loadpkl('./pickled.pkz', versioning=True)
 
-        
+
 def test_unversioned_pklization(tmpdir):
     tmpdir.chdir()